Download classification of intra- and intermolecular forces

3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
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LECTURE 8: INTRODUCTION TO INTRA- AND
INTERMOLECULAR FORCES
Outline :
LAST TIME : SINGLE CELL MECHANICS .............................................................................................. 2
CLASSIFICATION OF INTRA- AND INTERMOLECULAR FORCES ...................................................... 3
SPECIFIC TYPES OF INTRA- AND INTERMOLECULAR FORCES ....................................................... 4
HYDROPHOBIC / HYDROPHILIC INTERACTIONS................................................................................ 5
EXAMPLES .......................................................................................................................................... 6-7
Biological : Noncovalent Interactions in Folded Protein Structures .............................................. 6
Synthetic : Self-Assembling Peptide Amphiphiles for Regenerative Medicine ............................. 7
Objectives: To explore the qualitative origins of intra- and intermolecular forces
Readings: Course Reader documents 16-19, Links on "Supplementary Resources" section of
Stellar (Optional)
Multimedia : Protein folding demo posted on stellar; Lecture 8 : Bonding and protein structure
(California Lutheran University)
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3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
SINGLE CELL MECHANICS
-single cell AFM imaging
-motivation (musculoskeletal tissue, circulatory system, brain)
-experimental methods 1) localized area of the cell is deformed AFM, magnetic bead, 2) mechanical loading of an entire
cell micropipette aspiration, optical trap, 3) simultaneous mechanical loading of a population of cells (shear flow, cell force
monitor)
-cell modeling (Dao, et al 2003 J. Mech. Phys. Solids.)
• The composite is modeled as an isotropic, elastic, continuum, incompressible (constant volume), constant surface area
Constitutive Law : stress vs. strain relationship that describes a particular material
3=0 (always)=F/Ao
h
Single macromolecule Gaussian linear elastic Hookean spring F=kr →
summing over a network of random coil molecules
1 (applied)
"Triangulated Network"
(Lo )2
[1] Mohandas, et al. Mechanical properties of the red cell
membrane in relation to molecular structures and genetic
defects. Annu. Rec. Biophys. Struct. 1994. 23:787-818
(Lo )1
2=0 (by choice)
U
Strain energy of a 3D rubber elastic network
=
Go
12   23   3 2 - 3  

2
Neo-Hookean Rubber Elasticitry
 = extension or stretch ratio, 1 =
3
nonGaussian Nonlinear Strain Hardening Term
 L f 3
L f 1
L 
,  2 = f 2 , 3 =
Lo 1
 L o 2
 L o 3
Go  shear modulus
uniaxial normal stress, (N/m
=)2
n
C3  12   23   3 2 - 3 
by definition
U
1
constant volume constraint = 1 2  3 from definition of extension ratio & geometry
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3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
CLASSIFICATION OF INTRA- AND INTERMOLECULAR FORCES
(within individual molecules) (between individual molecules)
-Definitions : Interaction (more general), force (push or pull), bond (the attraction between atoms in a molecule or
crystalline structure)→ all intra- and intermolecular forces are electrostatic in origin → key to life on earth (e.g. water, cell
membranes, protein folding, etc.)
-strength measured relative to the thermal energy (room temperature) : kBT= 4.1 ● 10-21 J : "ruler"
noncovalent
I.
Primary or Chemical
● individually strong > kBT
● outer orbital e- shared that the discrete
nature of the atom is lost
● quantum mechanical in origin
● covalent → possess specificity,
directionality, stoichiometry
● metallic → delocalized electrons
II.
Secondary or Physical
● individually weak ≤ kBT
● no e- sharing; between two or
more atoms so discrete nature of
atoms
preserved
● more subtle attraction in origin
between (+) and (-) charges typically
lack specificity, directionality,
stoichiometry
III.
"Special"
● broad range of strength
● controversial
● not a "true" bond
hydrophobic, hydrophilic,
polymer effects (e.g. excluded
volume, entropic elasticity),
electrostatic double layer)
covalent, metallic, ionic (in air)
ionic (in water), polar,
polarization, dispersion
- Biological systems and bottom-up self-assembly is based on the balance and interplay of intra- and intermolecular forces.
-Noncovalent interactions allow for dynamic systems, i.e. breaking reversible reforming bonds doesn't require much
energy)/individually weak, forces are cumulative → stable in parallel.
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3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
SPECIFIC TYPES OF INTRA- AND INTERMOLECULAR FORCES
Ionic
-
+
-Coulombic attraction between oppositely charged species
-individually strong, however greatly weakened in the presence of water (e.g.
center of proteins→strong, DNA-proteins)
Polar Interactions
polar = asymmetric distribution of charge
● attractive force between an ion and a permanent dipole or two permanent
dipoles where the (+) charge attracts (-) (e.g. hydrogen bonds)

(-all 3 atoms in water can H-bond, up to 4 per molecule, important in biology
because it is able to form weak interactions with so many different chemical
species)
-
+
-
-
+
+
Polarization Interactions
+
-
-
● an ion or dipole in the vicinity of a nonpolar atom or molecule causes an
instantaneous polarization and electrostatic attraction
+
+
larger the e- cloud easier to distort (> polarizability)
London Dispersion
● nonpolar-nonpolar and induced dipole - induced dipole
● charge fluctuation, the (+) nucleus of a nonpolar atom attracts the (-)
charged electron cloud of another nonpolar atom → an instantaneous
induced, short lived fluctuating dipole, -takes place in all atoms / molecules,
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3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
HYDROPHOBIC ("WATER FEARING") INTERACTIONS
● attraction and association
between nonpolar molecules
in aqueous solution caused
by their inability to form Hbonds with water so as to
minimize disruption of Hbonds in water (nondirectional, entropy driven
since water has a more
ordered structure around
nonpolar molecules)
●e.g. alkanes, hydrocarbons, fluorocarbons, inert
atoms
●can be long range
●Conversely hydrophilic interactions result in
repulsion in order to maximize their interaction with
water, amphiphile- having both hydrophilic and
hydrophobic chemical constituents, solvophobic
(fearing other solvents)
●→ important for fouling/biocompatibility of
implanted devices, protein folding
http://en.wikipedia.org/wiki/Image:Dew_2.jpg
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3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
NONCOVALENT INTERACTIONS IN FOLDED PROTEINS
Human Serum Albumin
Random coil
→
balance
between
entopic
elasticity
and
noncovale
nt
attractive
forces
Hierachical levels :
1) Chemical : peptide bonds)
2) Primary : sequence of
amino acids
3) Secondary : local chain
configuration (-helix, sheet), loops
4) Tertiary : additional chain
folding over longer distances
5) Quaternary : globular
domains
6) Modular : linear array of
covalently attached domains
in series
Adapted from Grosberg and Khokhlov, Giant Molecules
PR
IN
I
OT
AM
A
E
I
A
"denatured" biologically inactive
AM
PR OT
E
IN
"native" state biologically active
→DEMO : Noncovalent interactions in proteins, chymotrypsin ( digestive proteolytic enzyme, catalyzes chemical reactions
to break down proteins into amino acids)
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3.052 Nanomechanics of Materials and Biomaterials Tuesday 03/06/07
Prof. C. Ortiz, MIT-DMSE
SELF-ASSEMBLING PEPTIDE AMPHIPHILES FOR REGENERATIVE MEDICINE
Hartgerink, et al. Science, 2001 "Self-assembly and mineralization of peptide-amphiphile nanofibers"
1) alkyl tail = hydrophobic promotes
self-organization
2) cysteines used for polymerization
of sulfides
3) flexible linker to give some molecular mobility
4) phosphorylated serine interacts
with calcium ions and promotes
mineralization
5) cell adhesion ligand RGD
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